I am trying to develop a laboratory test for genotyping patients on a SNP site. The polymorphism does not cause any change in restriction site (using online restriction mapping tool). The sequence is very repetitive and poor in GC. Allele specific primers are being tried but, looking for alternative solutions. Any suggestion is appreciated ?

 

Thank you

ahmer11

When you say allele specific primers, are you referring to allele specific oligonucleotides (because if not, then I would suggest this method! There's a slight semantic difference between primer and oligonucleotide, which has to do with how you use them).

 

Other than that, you're likely going to have to do a lot of sequencing (you could amplify a really short fragment to speed up the process, as long as you know exactly where the SNP is supposed to be).